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The values in the table below are normalized so that the most hydrophobic residue is given a value of 100 relative to glycine, which is considered neutral (0 value). In a protein, hydrophobic amino acids are likely to be found in the interior, whereas hydrophilic amino acids are likely to be in contact with the aqueous environment. DELTA-BLAST constructs a PSSM using the results of a Conserved Domain Database search and searches a sequence database. PHI-BLAST performs the search but limits alignments to those that match a pattern in the query. The hydrophobicity index is a measure of the relative hydrophobicity, or how soluble an amino acid is in water. PSI-BLAST allows the user to build a PSSM (position-specific scoring matrix) using the results of the first BlastP run. Hydrophobicity Index for Common Amino Acids Peptide Hydrophobicity/Hydrophilicity Analysis: Sequence:ġ-Pyrenemethylamine HCL Abz Abz/DNP Abz/Tyr (3-NO2) Amide Cyclic BOC DABCYL DABCYL/Glu(EDANS)-NH2 Double Disulfide bridge EDANS/DABCYL Glu(EDANS)-NH2 MCA/DNP mini-PEG1 mini-PEG2 Mono Disulfide bridge P-Nitroanilide Succinylation Triple Disulfide bridge Tyr (3-NO2)Īmino Acids with Hydrophobic Side Chain - AliphaticĪmino Acids with Hydrophobic Side Chain - AromaticĪmino Acids with Polar Neutral Side ChainsĪmino Acids with Electricaly Charged Side Chains - AcidicĪmino Acids with Electricaly Charged Side Chains - Basic Peptide Synthesis Application and Recommended Purity.Peptide Synthesis Frequently Asked Questions.Reverse Translation of Amino Acid Sequences.Amino Acid Converter: Three-letter to One-letter and One-letter to Three-letter.Peptide Synthesis Hydrophobicity Hydrophilicity Analysis.Peptide Synthesis for Peptide Array/Library.Peptide Hydrophobicity/Hydrophilicity Analysis Tool